I like wound on the thrown since it keeps up savage combat on all targets. no idea if it does more damage than instant, but keeping up savage combat would outweigh any advantage instant has since it buffs your fok damage and all your hunter's multi shot damage.

Instant Poison Main Hand. Deadly Poison Offhand
Thrown is Deadly if what you are aoeing will last long enough to reach a 5 stack, and Instant Poison otherwise (most trash is Deadly, rag adds during p2 are instant).

Also, if you haven't already, grab the Poisoner addon from Curse. It's quite handy for Rogues. I mainly like it for its auto-buy on Poisons feature. Makes sure I always keep a full stock (which for me is usually 20 instant and 40 deadly).

You don't use instant on your thrown weapon ever as combat. Wound Poison will outdps instant. For combat you only use instant on the main hand because of the deadly poisons mechanics (aka apply your main hand poison after 5 stacks), otherwise you'd also use wound poison there for more damage.
So, for FoK: Wound if targets live less than 30s, Deadly if targets live longer than 30s.